DS_Store and Mantis files included in cell table generation

[rdj71]

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Using a mac to run nimbus.predict_fovs(), I ran into an error that .DS_Store files could not be found, and ran into another error about .mantisDB files not found. I ran a script to remove all .DS_Store files that fixed the issue, and also ran a script to remove all .mantisDB files. After doing so, the cell_table was generated, but if trying to regenerate the cell_table, there is another .DS_Store file still in the directory that I needed to remove again.

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[JLrumberger]

Hi @rdj71,

thanks for raising this issue. I'll fix it ASAP.

Best,
Lorenz

[JLrumberger]

Hi @rdj71,

could it be that your problem can be fixed by just excluding the '.DS_Store' and '.mantisDB' paths from fov_paths after this line in the inference notebook: fov_paths = [os.path.join(tiff_dir, fov_name) for fov_name in fov_names]? If not, can lay out the folder structure? I was assuming something like this, where would the folders causing the problem be in this structure?

|-- base_dir
|   |-- image_data
|   |   |-- fov_1
|   |   |-- fov_2
|   |-- segmentation
|   |   |-- deepcell_output
|   |   |   |-- fov_1_whole_cell.tiff
|   |   |   |-- fov_2_whole_cell.tiff
|   |-- nimbus_output